lib/maf.c File Reference

#include "common.h"
#include "linefile.h"
#include "errabort.h"
#include "obscure.h"
#include "dnautil.h"
#include "axt.h"
#include "maf.h"
#include "hash.h"
#include <fcntl.h>

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Functions
mafFile *	mafMayOpen (char *fileName)
mafFile *	mafOpen (char *fileName)
void	mafRewind (struct mafFile *mf)
static boolean	nextLine (struct lineFile *lf, char **pLine)
mafAli *	mafNextWithPos (struct mafFile *mf, off_t *retOffset)
mafAli *	mafNext (struct mafFile *mf)
mafFile *	mafReadAll (char *fileName)
void	mafWriteStart (FILE *f, char *scoring)
void	mafWrite (FILE *f, struct mafAli *ali)
void	mafWriteEnd (FILE *f)
void	mafWriteAll (struct mafFile *mf, char *fileName)
void	mafCompFree (struct mafComp **pObj)
void	mafCompFreeList (struct mafComp **pList)
int	mafPlusStart (struct mafComp *comp)
void	mafAliFree (struct mafAli **pObj)
void	mafAliFreeList (struct mafAli **pList)
void	mafFileFree (struct mafFile **pObj)
void	mafFileFreeList (struct mafFile **pList)
mafComp *	mafMayFindComponent (struct mafAli *maf, char *src)
mafComp *	mafMayFindComponentDb (struct mafAli *maf, char *db)
mafComp *	mafFindComponent (struct mafAli *maf, char *src)
mafComp *	mafMayFindCompSpecies (struct mafAli *maf, char *species, char sepChar)
mafComp *	mafFindCompSpecies (struct mafAli *maf, char *species, char sepChar)
mafComp *	mafMayFindCompPrefix (struct mafAli *maf, char *pre, char *sep)
mafComp *	mafFindCompPrefix (struct mafAli *maf, char *pre, char *sep)
mafComp *	mafMayFindComponentInHash (struct mafAli *maf, struct hash *cHash)
boolean	mafMayFindAllComponents (struct mafAli *maf, struct hash *cHash)
mafAli *	mafSubset (struct mafAli *maf, char *componentSource, int newStart, int newEnd)
mafAli *	mafSubsetE (struct mafAli *maf, char *componentSource, int newStart, int newEnd, bool getInitialDashes)
void	mafMoveComponentToTop (struct mafAli *maf, char *componentSource)
boolean	mafNeedSubset (struct mafAli *maf, char *componentSource, int newStart, int newEnd)
void	mafFlipStrand (struct mafAli *maf)
void	mafSrcDb (char *name, char *retDb, int retDbSize)
boolean	mafColumnEmpty (struct mafAli *maf, int col)
void	mafStripEmptyColumns (struct mafAli *maf)
Variables
static char const	rcsid [] = "$Id: maf.c,v 1.34 2007/04/12 18:54:23 rico Exp $"

---

Function Documentation

void mafAliFree

(

struct mafAli **

pObj

)

Definition at line 378 of file maf.c.

References mafAli::components, freez(), and mafCompFreeList().

Referenced by mafAliFreeList().

{
struct mafAli *obj = *pObj;
if (obj == NULL)
    return;
mafCompFreeList(&obj->components);
freez(pObj);
}

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void mafAliFreeList

(

struct mafAli **

pList

)

Definition at line 388 of file maf.c.

References mafAliFree(), and mafAli::next.

Referenced by mafFileFree().

{
struct mafAli *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    mafAliFree(&el);
    }
*pList = NULL;
}

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boolean mafColumnEmpty	(	struct mafAli *	maf,
		int	col
	)

Definition at line 703 of file maf.c.

References mafAli::components, FALSE, mafComp::next, mafComp::text, and TRUE.

Referenced by mafStripEmptyColumns().

{
assert(col < maf->textSize);
struct mafComp *comp;
for (comp = maf->components; comp != NULL; comp = comp->next)
    {
    char c = comp->text[col];
    if (c != '.' && c != '-')
        return FALSE;
    }
return TRUE;
}

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void mafCompFree

(

struct mafComp **

pObj

)

Definition at line 344 of file maf.c.

References freeMem(), freez(), mafComp::quality, mafComp::src, and mafComp::text.

Referenced by mafCompFreeList().

{
struct mafComp *obj = *pObj;
if (obj == NULL)
    return;
freeMem(obj->src);
freeMem(obj->text);
freeMem(obj->quality);
freez(pObj);
}

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void mafCompFreeList

(

struct mafComp **

pList

)

Definition at line 356 of file maf.c.

References mafCompFree(), and mafComp::next.

Referenced by mafAliFree().

{
struct mafComp *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    mafCompFree(&el);
    }
*pList = NULL;
}

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void mafFileFree

(

struct mafFile **

pObj

)

Definition at line 401 of file maf.c.

References mafFile::alignments, freeMem(), freez(), mafFile::lf, lineFileClose(), mafAliFreeList(), and mafFile::scoring.

Referenced by mafFileFreeList().

{
struct mafFile *obj = *pObj;
if (obj == NULL)
    return;
lineFileClose(&obj->lf);
freeMem(obj->scoring);
mafAliFreeList(&obj->alignments);
freez(pObj);
}

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void mafFileFreeList

(

struct mafFile **

pList

)

Definition at line 413 of file maf.c.

References mafFileFree(), and mafFile::next.

{
struct mafFile *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    mafFileFree(&el);
    }
*pList = NULL;
}

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struct mafComp* mafFindComponent	(	struct mafAli *	maf,
		char *	src
	)			[read]

Definition at line 459 of file maf.c.

References errAbort(), and mafMayFindComponent().

Referenced by mafMoveComponentToTop(), mafNeedSubset(), and mafSubsetE().

{
struct mafComp *mc = mafMayFindComponent(maf, src);
if (mc == NULL)
    errAbort("Couldn't find %s in maf", src);
return mc;
}

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struct mafComp* mafFindCompPrefix	(	struct mafAli *	maf,
		char *	pre,
		char *	sep
	)			[read]

Definition at line 518 of file maf.c.

References errAbort(), and mafMayFindCompPrefix().

{
struct mafComp *mc = mafMayFindCompPrefix(maf, pre, sep);
if (mc == NULL)
    errAbort("Couldn't find %s%s... in maf", pre,sep);
return mc;
}

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struct mafComp* mafFindCompSpecies	(	struct mafAli *	maf,
		char *	species,
		char	sepChar
	)			[read]

Definition at line 489 of file maf.c.

References errAbort(), and mafMayFindCompSpecies().

{
struct mafComp *mc = mafMayFindCompSpecies(maf, species, sepChar);
if (mc == NULL)
    errAbort("Couldn't find %s%c or just %s... in maf", species,sepChar,species);
return mc;
}

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void mafFlipStrand

(

struct mafAli *

maf

)

Definition at line 664 of file maf.c.

References mafAli::components, mafComp::leftLen, mafComp::leftStatus, mafComp::next, mafComp::quality, reverseBytes(), reverseComplement(), reverseIntRange(), mafComp::rightLen, mafComp::rightStatus, mafComp::size, mafComp::srcSize, mafComp::start, mafComp::strand, mafComp::text, and mafAli::textSize.

{
struct mafComp *mc;
for (mc = maf->components; mc != NULL; mc = mc->next)
    {
    int e = mc->start + mc->size;
    reverseIntRange(&mc->start, &e, mc->srcSize);
    if (mc->text != NULL)
        reverseComplement(mc->text, maf->textSize);
        if (mc->quality != NULL)
                reverseBytes(mc->quality, maf->textSize);
    if (mc->strand == '-')
        mc->strand = '+';
    else
        mc->strand = '-';
    char holdStatus = mc->leftStatus;
    mc->leftStatus = mc->rightStatus;
    mc->rightStatus = holdStatus;
    int holdLen = mc->leftLen;
    mc->leftLen = mc->rightLen;
    mc->rightLen = holdLen;
    }
}

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boolean mafMayFindAllComponents	(	struct mafAli *	maf,
		struct hash *	cHash
	)

Definition at line 542 of file maf.c.

References FALSE, hashFirst(), hashNext(), mafMayFindComponent(), hashEl::name, and TRUE.

{
struct hashCookie cookie = hashFirst(cHash);
struct hashEl *el;

while ((el = hashNext(&cookie)) != NULL)
    if (mafMayFindComponent(maf, el->name) == NULL)
        return FALSE;
return TRUE;
}

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struct mafComp* mafMayFindComponent	(	struct mafAli *	maf,
		char *	src
	)			[read]

Definition at line 426 of file maf.c.

References mafAli::components, mafComp::next, sameString, and mafComp::src.

Referenced by mafFindComponent(), and mafMayFindAllComponents().

{
struct mafComp *mc;
for (mc = maf->components; mc != NULL; mc = mc->next)
    {
    if (sameString(mc->src, src))
        return mc;
    }
return NULL;
}

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struct mafComp* mafMayFindComponentDb	(	struct mafAli *	maf,
		char *	db
	)			[read]

Definition at line 438 of file maf.c.

References mafAli::components, mafComp::next, and mafComp::src.

{
struct mafComp *mc;
char *p, *q;
for (mc = maf->components; mc != NULL; mc = mc->next)
    {
    for (p = mc->src, q = db; *p && *q; p++, q++)
        {
        if (*p != *q)
            break;
        }
    if (*p == '.' && *q == 0)
        return mc;
    if (*p == *q)
        return mc;
    }
return NULL;
}

struct mafComp* mafMayFindComponentInHash	(	struct mafAli *	maf,
		struct hash *	cHash
	)			[read]

Definition at line 528 of file maf.c.

References mafAli::components, hashFindVal(), mafComp::next, and mafComp::src.

{
struct mafComp *mc;

for (mc = maf->components; mc != NULL; mc = mc->next)
    {
    if (hashFindVal(cHash, mc->src))
        return mc;
    }
return NULL;
}

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struct mafComp* mafMayFindCompPrefix	(	struct mafAli *	maf,
		char *	pre,
		char *	sep
	)			[read]

Definition at line 499 of file maf.c.

References mafAli::components, mafComp::next, mafComp::src, and startsWith().

Referenced by mafFindCompPrefix().

{
struct mafComp *mc;
char prefix[256];

if (sep == NULL)
    sep = "";
snprintf(prefix, 256, "%s%s", pre, sep);

for (mc = maf->components; mc != NULL; mc = mc->next)
    {
    if (startsWith(prefix, mc->src))
        return mc;
    }
return NULL;
}

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struct mafComp* mafMayFindCompSpecies	(	struct mafAli *	maf,
		char *	species,
		char	sepChar
	)			[read]

Definition at line 468 of file maf.c.

References mafAli::components, mafComp::next, mafComp::src, and startsWith().

Referenced by mafFindCompSpecies().

{
struct mafComp *mc;
int speciesLen = strlen(species);

for (mc = maf->components; mc != NULL; mc = mc->next)
    {
    if (startsWith(species, mc->src) )
        {
        char endChar = mc->src[speciesLen];

        if ((endChar == '\0') || (endChar == sepChar))
            return mc;
        }
    }
return NULL;
}

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struct mafFile* mafMayOpen

(

char *

fileName

)

[read]

Definition at line 14 of file maf.c.

References AllocVar, cloneString(), errAbort(), mafFile::lf, lineFileMayOpen(), lineFileNeedNext(), name, nextWord(), sameString, mafFile::scoring, startsWith(), TRUE, and mafFile::version.

Referenced by mafOpen().

{
struct mafFile *mf;
struct lineFile *lf;
char *line, *word;
char *sig = "##maf";

if ((lf = lineFileMayOpen(fileName, TRUE)) == NULL)
    return NULL;
AllocVar(mf);
mf->lf = lf;

lineFileNeedNext(lf, &line, NULL);
if (!startsWith(sig, line))
    {
    errAbort("%s does not start with %s", fileName, sig);
    }
line += strlen(sig);

while ((word = nextWord(&line)) != NULL)
    {
    /* Parse name=val. */
    char *name = word;
    char *val = strchr(word, '=');
    if (val == NULL)
       errAbort("Missing = after %s line 1 of %s\n", name, fileName);
    *val++ = 0;

    if (sameString(name, "version"))
        mf->version = atoi(val);
    else if (sameString(name, "scoring"))
        mf->scoring = cloneString(val);
    }
if (mf->version == 0)
    errAbort("No version line 1 of %s\n", fileName);
return mf;
}

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void mafMoveComponentToTop	(	struct mafAli *	maf,
		char *	componentSource
	)

Definition at line 642 of file maf.c.

References mafAli::components, mafFindComponent(), slAddHead, and slRemoveEl().

{
struct mafComp *mcMaster = mafFindComponent(maf, componentSource);
slRemoveEl(&maf->components, mcMaster);
slAddHead(&maf->components, mcMaster);
}

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boolean mafNeedSubset	(	struct mafAli *	maf,
		char *	componentSource,
		int	newStart,
		int	newEnd
	)

Definition at line 650 of file maf.c.

References mafFindComponent(), reverseIntRange(), mafComp::size, mafComp::srcSize, mafComp::start, and mafComp::strand.

{
struct mafComp *mcMaster = mafFindComponent(maf, componentSource);

/* Reverse complement input range if necessary. */
if (mcMaster->strand == '-')
    reverseIntRange(&newStart, &newEnd, mcMaster->srcSize);

return newStart > mcMaster->start || newEnd < mcMaster->start + mcMaster->size;
}

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struct mafAli* mafNext

(

struct mafFile *

mf

)

[read]

Definition at line 235 of file maf.c.

References mafNextWithPos().

Referenced by mafReadAll().

{
return mafNextWithPos(mf, NULL);
}

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struct mafAli* mafNextWithPos	(	struct mafFile *	mf,
		off_t *	retOffset
	)			[read]

Definition at line 82 of file maf.c.

References AllocVar, ArraySize, chopByWhite(), cloneString(), mafAli::components, errAbort(), lineFile::fileName, mafComp::leftLen, mafComp::leftStatus, mafFile::lf, lineFileClose(), lineFileExpectWords(), lineFileNeedNum(), lineFileTell, lineFile::lineIx, name, nextLine(), nextWord(), mafComp::quality, mafComp::rightLen, mafComp::rightStatus, sameString, mafAli::score, slAddHead, slReverse(), mafComp::src, and mafAli::textSize.

Referenced by mafNext().

{
struct lineFile *lf = mf->lf;
struct mafAli *ali;
char *line, *word;

/* Loop until get an alignment paragraph or reach end of file. */
for (;;)
    {
    /* Get alignment header line.  If it's not there assume end of file. */
    if (!nextLine(lf, &line))
        {
        lineFileClose(&mf->lf);
        return NULL;
        }

    /* Parse alignment header line. */
    word = nextWord(&line);
    if (word == NULL)
        continue;       /* Ignore blank lines. */
        
    if (sameString(word, "a"))
        {
        if (retOffset != NULL)
            *retOffset = lineFileTell(mf->lf);
        AllocVar(ali);
        while ((word = nextWord(&line)) != NULL)
            {
            /* Parse name=val. */
            char *name = word;
            char *val = strchr(word, '=');
            if (val == NULL)
               errAbort("Missing = after %s line 1 of %s", name, lf->fileName);
            *val++ = 0;

            if (sameString(name, "score"))
                ali->score = atof(val);
            }

        /* Parse alignment components until blank line. */
        for (;;)
            {
            if (!nextLine(lf, &line))
                errAbort("Unexpected end of file %s", lf->fileName);
            word = nextWord(&line);
            if (word == NULL)
                break;
            if (sameString(word, "s") || sameString(word, "e"))
                {
                struct mafComp *comp;
                int wordCount;
                char *row[7];
                int textSize;

                /* Chop line up by white space.  This involves a few +-1's because
                 * have already chopped out first word. */
                row[0] = word;
                wordCount = chopByWhite(line, row+1, ArraySize(row)-1) + 1; /* +-1 because of "s" */
                lineFileExpectWords(lf, ArraySize(row), wordCount);
                AllocVar(comp);

                /* Convert ascii text representation to mafComp structure. */
                comp->src = cloneString(row[1]);
                comp->srcSize = lineFileNeedNum(lf, row, 5);
                comp->strand = row[4][0];
                comp->start = lineFileNeedNum(lf, row, 2);

                if (sameString(word, "e"))
                    {
                    comp->size = 0;
                    comp->rightLen = comp->leftLen = lineFileNeedNum(lf, row, 3);
                    comp->rightStatus = comp->leftStatus = *row[6];
                    }
                else
                    {
                    comp->size = lineFileNeedNum(lf, row, 3);
                    comp->text = cloneString(row[6]);
                    textSize = strlen(comp->text);

                    /* Fill in ali->text size. */
                    if (ali->textSize == 0)
                        ali->textSize = textSize;
                    else if (ali->textSize != textSize)
                        errAbort("Text size inconsistent (%d vs %d) line %d of %s",
                            textSize, ali->textSize, lf->lineIx, lf->fileName);
                    }

                /* Do some sanity checking. */
                if (comp->srcSize < 0 || comp->size < 0)
                     errAbort("Got a negative size line %d of %s", lf->lineIx, lf->fileName);
                if (comp->start < 0 || comp->start + comp->size > comp->srcSize)
                     errAbort("Coordinates out of range line %d of %s", lf->lineIx, lf->fileName);
                  
                /* Add component to head of list. */
                slAddHead(&ali->components, comp);
                }
            if (sameString(word, "i"))
                {
                struct mafComp *comp;
                int wordCount;
                char *row[6];

                /* Chop line up by white space.  This involves a few +-1's because
                 * have already chopped out first word. */
                row[0] = word;
                wordCount = chopByWhite(line, row+1, ArraySize(row)-1) + 1; /* +-1 because of "s" */
                lineFileExpectWords(lf, ArraySize(row), wordCount);
                if (!sameString(row[1],ali->components->src))
                    errAbort("i line src mismatch: i is %s :: s is %s\n", row[1], ali->components->src);

                comp = ali->components;
                comp->leftStatus = *row[2];
                comp->leftLen = atoi(row[3]);
                comp->rightStatus = *row[4];
                comp->rightLen = atoi(row[5]);
                }
                if (sameString(word, "q"))
                {
                struct mafComp *comp;
                int wordCount;
                char *row[3];

                /* Chop line up by white space.  This involves a few +-1's because
                 * have already chopped out first word. */
                row[0] = word;
                wordCount = chopByWhite(line, row+1, ArraySize(row)-1) + 1; /* +-1 because of "s" */
                lineFileExpectWords(lf, ArraySize(row), wordCount);
                if (!sameString(row[1],ali->components->src))
                    errAbort("q line src mismatch: q is %s :: s is %s\n", row[1], ali->components->src);

                        comp = ali->components;
                        comp->quality = cloneString(row[2]);
                }
            }
        slReverse(&ali->components);
        return ali;
        }
    else  /* Skip over paragraph we don't understand. */
        {
        for (;;)
            {
            if (!nextLine(lf, &line))
                return NULL;
            if (nextWord(&line) == NULL)
                break;
            }
        }
    }
}

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struct mafFile* mafOpen

(

char *

fileName

)

[read]

Definition at line 53 of file maf.c.

References errnoAbort(), and mafMayOpen().

Referenced by mafReadAll().

{
struct mafFile *mf = mafMayOpen(fileName);
if (mf == NULL)
    errnoAbort("Couldn't open %s\n", fileName);
return mf;
}

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int mafPlusStart

(

struct mafComp *

comp

)

Definition at line 369 of file maf.c.

References mafComp::size, mafComp::srcSize, mafComp::start, and mafComp::strand.

{
if (comp->strand == '-') 
    return comp->srcSize - (comp->start + comp->size);
else
    return comp->start;
}

struct mafFile* mafReadAll

(

char *

fileName

)

[read]

Definition at line 242 of file maf.c.

References mafFile::alignments, mafNext(), mafOpen(), slAddHead, and slReverse().

{
struct mafFile *mf = mafOpen(fileName);
struct mafAli *ali;
while ((ali = mafNext(mf)) != NULL)
    {
    slAddHead(&mf->alignments, ali);
    }
slReverse(&mf->alignments);
return mf;
}

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void mafRewind

(

struct mafFile *

mf

)

Definition at line 62 of file maf.c.

References errAbort(), mafFile::lf, lineFileSeek(), and SEEK_SET.

{
if (mf == NULL)
    errAbort("maf file rewind failed -- file not open");
lineFileSeek(mf->lf, 0, SEEK_SET);
}

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void mafSrcDb	(	char *	name,
		char *	retDb,
		int	retDbSize
	)

Definition at line 689 of file maf.c.

{
int len;
char *e = strchr(name, '.');
/* Put prefix up to dot into buf. */
len = (e == NULL ? strlen(name) : e - name);
if (len >= retDbSize)
     len = retDbSize-1;
memcpy(retDb, name, len);
retDb[len] = 0;
}

void mafStripEmptyColumns

(

struct mafAli *

maf

)

Definition at line 717 of file maf.c.

References mafAli::components, mafColumnEmpty(), mafComp::next, mafComp::quality, mafComp::text, and mafAli::textSize.

{
/* Selectively copy over non-empty columns. */
int readIx=0, writeIx = 0;
struct mafComp *comp;
for (readIx=0; readIx < maf->textSize; ++readIx)
    {
    if (!mafColumnEmpty(maf, readIx))
        {
                for (comp = maf->components; comp != NULL; comp = comp->next) 
                        {
                    comp->text[writeIx] = comp->text[readIx];
                        if (comp->quality != NULL)
                                comp->quality[writeIx] = comp->quality[readIx];
                        }
                ++writeIx;
                }
    }

/* Zero terminate text, and update textSize. */
for (comp = maf->components; comp != NULL; comp = comp->next)
        {
    comp->text[writeIx] = 0;
        if (comp->quality != NULL)
                comp->quality[writeIx] = 0;
        }
maf->textSize = writeIx;
}

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struct mafAli* mafSubset	(	struct mafAli *	maf,
		char *	componentSource,
		int	newStart,
		int	newEnd
	)			[read]

Definition at line 555 of file maf.c.

References FALSE, and mafSubsetE().

{
return mafSubsetE(maf, componentSource, newStart, newEnd, FALSE);
}

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struct mafAli* mafSubsetE	(	struct mafAli *	maf,
		char *	componentSource,
		int	newStart,
		int	newEnd,
		bool	getInitialDashes
	)			[read]

Definition at line 561 of file maf.c.

References AllocVar, cloneString(), cloneStringZ(), mafAli::components, countNonDash(), mafComp::leftLen, mafComp::leftStatus, mafFindComponent(), mafComp::next, mafComp::quality, reverseIntRange(), mafComp::rightLen, mafComp::rightStatus, mafComp::size, skipIgnoringDash(), slAddHead, slReverse(), mafComp::src, mafComp::srcSize, mafComp::start, mafComp::strand, mafComp::text, mafAli::textSize, and TRUE.

Referenced by mafSubset().

{
struct mafComp *mcMaster = mafFindComponent(maf, componentSource);
struct mafAli *subset;
struct mafComp *mc, *subMc;
char *s, *e;
int textStart, textSize;

/* Reverse complement input range if necessary. */
if (mcMaster->strand == '-')
    reverseIntRange(&newStart, &newEnd, mcMaster->srcSize);

/* Check if any real intersection and return NULL if not. */
if (newStart >= newEnd)
    return NULL;
if (newStart >= mcMaster->start + mcMaster->size)
    return NULL;
if (newEnd <= mcMaster->start)
    return NULL;

/* Clip to bounds of actual data. */
if (newStart < mcMaster->start)
    newStart = mcMaster->start;
if (newEnd > mcMaster->start + mcMaster->size)
    newEnd = mcMaster->start + mcMaster->size;

/* Translate position in master sequence to position in
 * multiple alignment. */
s = skipIgnoringDash(mcMaster->text, newStart - mcMaster->start, TRUE);
e = skipIgnoringDash(s, newEnd - newStart, TRUE);
textStart = s - mcMaster->text;
textSize = e - s;

if (getInitialDashes && (newStart == mcMaster->start))
    {
    textStart = 0;
    textSize += s - mcMaster->text;
    }

/* Allocate subset structure and fill it in */
AllocVar(subset);
subset->textSize = textSize;
for (mc = maf->components; mc != NULL; mc = mc->next)
    {
    AllocVar(subMc);
    subMc->src = cloneString(mc->src);
    subMc->srcSize = mc->srcSize;
    subMc->strand = mc->strand;
    if (mc->size != 0)
        {
        subMc->start = mc->start + countNonDash(mc->text, textStart);
        subMc->size = countNonDash(mc->text+textStart, textSize);
        subMc->text = cloneStringZ(mc->text + textStart, textSize);
                if (mc->quality != NULL)
                        subMc->quality = cloneStringZ(mc->quality + textStart, textSize);
        }
    else
        {
        /* empty row annotation */
        subMc->size = 0;
        subMc->start = mc->start;
        }
    subMc->leftStatus = mc->leftStatus;
    subMc->leftLen = mc->leftLen;
    subMc->rightStatus = mc->rightStatus;
    subMc->rightLen = mc->rightLen;
    slAddHead(&subset->components, subMc);
    }
slReverse(&subset->components);
return subset;
}

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void mafWrite	(	FILE *	f,
		struct mafAli *	ali
	)

Definition at line 265 of file maf.c.

References cloneString(), mafAli::components, digitsBaseTen(), mafComp::leftLen, mafComp::leftStatus, mafComp::next, mafComp::quality, mafComp::rightLen, mafComp::rightStatus, sameString, mafAli::score, mafComp::size, mafComp::src, mafComp::srcSize, mafComp::start, mafComp::strand, and mafComp::text.

Referenced by mafQueryOut(), and mafWriteAll().

{
struct mafComp *comp;
int srcChars = 0, startChars = 0, sizeChars = 0, srcSizeChars = 0;

/* Write out alignment header */
fprintf(f, "a score=%f\n", ali->score);

/* Figure out length of each field. */
for (comp = ali->components; comp != NULL; comp = comp->next)
    {
    int len = 0;
    /* a name like '.' will break some tools, so replace it
    * with a generic name */
    if (sameString(comp->src,"."))
        comp->src=cloneString("defaultName");
    len = strlen(comp->src);
    if (srcChars < len)
        srcChars = len;
    len = digitsBaseTen(comp->start);
    if (startChars < len)
        startChars = len;
    len = digitsBaseTen(comp->size);
    if (sizeChars < len)
        sizeChars = len;
    len = digitsBaseTen(comp->srcSize);
    if (srcSizeChars < len)
        srcSizeChars = len;
    }

/* Write out each component. */
for (comp = ali->components; comp != NULL; comp = comp->next)
    {
    if ((comp->size == 0) && (comp->leftStatus))
        fprintf(f, "e %-*s %*d %*d %c %*d %c\n", 
            srcChars, comp->src, startChars, comp->start, 
            sizeChars, comp->leftLen, comp->strand, 
            srcSizeChars, comp->srcSize, comp->leftStatus);
    else
        {
        fprintf(f, "s %-*s %*d %*d %c %*d %s\n", 
            srcChars, comp->src, startChars, comp->start, 
            sizeChars, comp->size, comp->strand, 
            srcSizeChars, comp->srcSize, comp->text);

        if (comp->quality)
                fprintf(f, "q %-*s %s\n",
                srcChars + startChars + sizeChars + srcSizeChars + 5,
                comp->src, comp->quality);

        if (comp->leftStatus)
            fprintf(f,"i %-*s %c %d %c %d\n",srcChars,comp->src,
                comp->leftStatus,comp->leftLen,comp->rightStatus,comp->rightLen);
        }

    }

/* Write out blank separator line. */
fprintf(f, "\n");
}

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void mafWriteAll	(	struct mafFile *	mf,
		char *	fileName
	)

Definition at line 332 of file maf.c.

References mafFile::alignments, carefulClose(), mafWrite(), mafWriteEnd(), mafWriteStart(), mustOpen(), mafAli::next, and mafFile::scoring.

{
FILE *f = mustOpen(fileName, "w");
struct mafAli *ali;
mafWriteStart(f, mf->scoring);
for (ali = mf->alignments; ali != NULL; ali = ali->next)
    mafWrite(f, ali);
mafWriteEnd(f);
carefulClose(&f);
}

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void mafWriteEnd

(

FILE *

f

)

Definition at line 327 of file maf.c.

Referenced by mafWriteAll().

{
}

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void mafWriteStart	(	FILE *	f,
		char *	scoring
	)

Definition at line 255 of file maf.c.

Referenced by mafHead(), and mafWriteAll().

{
fprintf(f, "##maf version=1");
if (scoring != NULL)
    fprintf(f, " scoring=%s", scoring);
fprintf(f, "\n");
}

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static boolean nextLine	(	struct lineFile *	lf,
		char **	pLine
	)			[static]

Definition at line 70 of file maf.c.

References FALSE, mafFile::lf, lineFileNext(), and TRUE.

Referenced by axtScoreSchemeFromProteinText(), gffGroupLines(), and mafNextWithPos().

{
for (;;)
    {
    if (!lineFileNext(lf, pLine, NULL))
        return FALSE;
    if (**pLine != '#')
        return TRUE;
    }
}

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---

Variable Documentation

char const rcsid[] = "$Id: maf.c,v 1.34 2007/04/12 18:54:23 rico Exp $" [static]

Definition at line 12 of file maf.c.

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